Calcium in PDB 6nuc: Structure of Calcineurin in Complex with NHE1 Peptide

All present enzymatic activity of Structure of Calcineurin in Complex with NHE1 Peptide:
3.1.3.16;

The structure of Structure of Calcineurin in Complex with NHE1 Peptide, PDB code: 6nuc was solved by X.Wang, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.97 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.549, 127.073, 127.421, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.4

The structure of Structure of Calcineurin in Complex with NHE1 Peptide also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iron	(Fe)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structure of Calcineurin in Complex with NHE1 Peptide (pdb code 6nuc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Calcineurin in Complex with NHE1 Peptide, PDB code: 6nuc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Calcineurin in Complex with NHE1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calcineurin in Complex with NHE1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:37.8 occ:1.00 OD1 B:ASN67 2.2 44.3 1.0 OE2 B:GLU74 2.3 35.3 1.0 O B:GLU69 2.3 38.6 1.0 OD1 B:ASP65 2.4 47.3 1.0 O B:HOH310 2.4 40.5 1.0 OE1 B:GLU74 2.4 36.5 1.0 OD1 B:ASP63 2.4 40.7 1.0 CD B:GLU74 2.7 35.9 1.0 CG B:ASP65 3.2 47.6 1.0 CG B:ASN67 3.3 50.0 1.0 CG B:ASP63 3.4 38.0 1.0 OD2 B:ASP65 3.4 55.4 1.0 HA B:ASP63 3.4 46.1 1.0 H B:ASN67 3.5 56.1 1.0 C B:GLU69 3.5 33.6 1.0 HD21 B:ASN67 3.6 58.6 1.0 H B:GLU69 3.6 45.2 1.0 H B:ASP65 3.6 48.1 1.0 HA B:VAL70 3.7 37.8 1.0 H B:ASP71 3.8 43.5 1.0 ND2 B:ASN67 3.8 48.8 1.0 CA B:ASP63 4.1 38.4 1.0 CB B:ASP63 4.2 34.3 1.0 CG B:GLU74 4.2 33.0 1.0 H B:GLY66 4.2 52.1 1.0 OD2 B:ASP71 4.2 50.2 1.0 OD2 B:ASP63 4.2 39.3 1.0 HB2 B:ASP63 4.2 41.1 1.0 N B:ASN67 4.3 46.8 1.0 N B:GLU69 4.3 37.7 1.0 N B:VAL70 4.4 32.5 1.0 CA B:VAL70 4.4 31.5 1.0 CB B:ASN67 4.4 44.8 1.0 N B:ASP65 4.4 40.1 1.0 O B:HOH314 4.5 44.7 1.0 N B:ASP71 4.5 36.2 1.0 CB B:ASP65 4.5 41.5 1.0 CA B:GLU69 4.5 43.5 1.0 C B:ASP63 4.5 34.5 1.0 HG3 B:GLU74 4.5 39.6 1.0 HB3 B:ASN67 4.5 53.7 1.0 N B:GLY66 4.6 43.4 1.0 H B:GLY68 4.6 51.7 1.0 HG2 B:GLU74 4.6 39.6 1.0 HB2 B:GLU69 4.6 46.1 1.0 HD22 B:ASN67 4.6 58.6 1.0 H B:THR64 4.7 42.3 1.0 N B:THR64 4.8 35.3 1.0 CA B:ASN67 4.8 39.0 1.0 HB3 B:ASP65 4.8 49.7 1.0 CA B:ASP65 4.8 40.8 1.0 C B:ASP65 4.8 47.1 1.0 N B:GLY68 4.9 43.1 1.0 HB2 B:GLU74 4.9 38.3 1.0 CG B:ASP71 4.9 39.5 1.0 C B:VAL70 4.9 38.0 1.0 HB3 B:ASP71 4.9 43.1 1.0 C B:ASN67 5.0 41.0 1.0

Calcium binding site 2 out of 4 in the Structure of Calcineurin in Complex with NHE1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calcineurin in Complex with NHE1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:32.4 occ:1.00 O B:ARG147 2.3 34.1 1.0 OD1 B:ASP143 2.3 35.0 1.0 OD1 B:ASP141 2.3 36.7 1.0 OD1 B:ASP145 2.3 34.3 1.0 O B:HOH321 2.5 34.1 1.0 OE1 B:GLU152 2.5 34.0 1.0 OE2 B:GLU152 2.5 37.4 1.0 CD B:GLU152 2.9 35.0 1.0 CG B:ASP143 3.2 44.9 1.0 CG B:ASP145 3.3 39.8 1.0 H B:ARG147 3.4 42.7 1.0 CG B:ASP141 3.5 35.2 1.0 OD2 B:ASP143 3.5 46.2 1.0 H B:ASP143 3.5 43.7 1.0 C B:ARG147 3.5 30.0 1.0 HA B:ASP141 3.6 35.8 1.0 H B:ASP145 3.6 39.4 1.0 OD2 B:ASP145 3.7 37.0 1.0 H B:SER149 3.7 37.3 1.0 HA B:ILE148 3.7 30.1 1.0 H B:LYS142 3.9 44.7 1.0 N B:ARG147 4.1 35.5 1.0 H B:GLY144 4.1 39.6 1.0 HG2 B:ARG147 4.2 51.5 1.0 HD13 B:ILE148 4.2 35.0 1.0 OD2 B:ASP141 4.2 33.7 1.0 H B:GLY146 4.3 39.2 1.0 HG3 B:ARG147 4.3 51.5 1.0 N B:ASP143 4.3 36.4 1.0 CA B:ASP141 4.3 29.8 1.0 N B:ASP145 4.3 32.9 1.0 CB B:ASP141 4.4 29.4 1.0 N B:ILE148 4.4 28.5 1.0 CG B:GLU152 4.4 30.0 1.0 N B:SER149 4.4 31.1 1.0 CA B:ARG147 4.4 34.6 1.0 CA B:ILE148 4.4 25.0 1.0 N B:LYS142 4.5 37.2 1.0 HB3 B:SER149 4.5 47.1 1.0 HB2 B:ASP141 4.5 35.3 1.0 CB B:ASP143 4.5 44.4 1.0 CB B:ASP145 4.6 38.3 1.0 N B:GLY144 4.6 33.0 1.0 N B:GLY146 4.6 32.7 1.0 CG B:ARG147 4.7 42.9 1.0 HG3 B:GLU152 4.7 36.0 1.0 HG2 B:GLU152 4.8 36.0 1.0 CA B:ASP143 4.8 38.2 1.0 C B:ASP141 4.8 39.3 1.0 CA B:ASP145 4.8 35.9 1.0 HB3 B:ASP145 4.8 46.0 1.0 HD1 B:TYR106 4.9 42.2 1.0 C B:ILE148 4.9 31.8 1.0 C B:ASP145 4.9 34.1 1.0 C B:ASP143 4.9 35.7 1.0 HB3 B:ASP143 4.9 53.3 1.0 HB2 B:GLU152 4.9 34.8 1.0 O B:HOH358 5.0 45.4 1.0

Calcium binding site 3 out of 4 in the Structure of Calcineurin in Complex with NHE1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Calcineurin in Complex with NHE1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:32.1 occ:1.00 O B:SER37 2.3 32.3 1.0 OD1 B:ASP33 2.3 36.7 1.0 OD1 B:ASP31 2.3 31.4 1.0 O B:HOH372 2.4 42.9 1.0 OE2 B:GLU42 2.4 34.8 1.0 OG B:SER35 2.5 34.6 1.0 OE1 B:GLU42 2.6 29.1 1.0 CD B:GLU42 2.8 35.5 1.0 H B:SER35 3.2 44.7 1.0 CG B:ASP33 3.3 38.9 1.0 CG B:ASP31 3.5 32.5 1.0 C B:SER37 3.5 29.0 1.0 H B:ASP33 3.6 35.7 1.0 H B:SER37 3.6 39.1 1.0 CB B:SER35 3.6 34.5 1.0 HA B:LEU38 3.7 34.5 1.0 HA B:ASP31 3.7 35.6 1.0 HB3 B:SER35 3.7 41.4 1.0 OD2 B:ASP33 3.8 41.8 1.0 H B:SER39 3.9 41.5 1.0 N B:SER35 4.0 37.3 1.0 HD23 B:LEU38 4.2 34.4 1.0 OD2 B:ASP31 4.3 31.9 1.0 N B:SER37 4.3 32.5 1.0 CA B:SER35 4.4 34.9 1.0 CG B:GLU42 4.4 36.7 1.0 HB2 B:SER35 4.4 41.4 1.0 CA B:ASP31 4.4 29.7 1.0 O B:HOH311 4.4 42.8 1.0 N B:ASP33 4.4 29.8 1.0 CA B:LEU38 4.4 28.7 1.0 N B:LEU38 4.4 32.9 1.0 H B:ASN34 4.4 38.2 1.0 CB B:ASP31 4.5 31.1 1.0 N B:SER39 4.5 34.5 1.0 H B:LEU32 4.5 36.9 1.0 CA B:SER37 4.5 34.3 1.0 C B:ASP31 4.5 28.8 1.0 HB3 B:SER39 4.6 43.6 1.0 CB B:ASP33 4.6 36.6 1.0 H B:GLY36 4.6 40.3 1.0 N B:ASN34 4.6 31.8 1.0 HG3 B:GLU42 4.6 44.0 1.0 N B:LEU32 4.7 30.7 1.0 HB2 B:SER37 4.8 46.4 1.0 HG2 B:GLU42 4.8 44.0 1.0 CA B:ASP33 4.8 32.7 1.0 C B:ASP33 4.8 29.4 1.0 HB2 B:ASP31 4.8 37.4 1.0 O B:HOH340 4.8 41.8 1.0 N B:GLY36 4.9 33.6 1.0 C B:SER35 4.9 32.5 1.0 HB3 B:ASP33 4.9 44.0 1.0 C B:LEU38 4.9 34.0 1.0 O B:HOH353 4.9 55.4 1.0 OE2 B:GLU69 4.9 52.0 1.0

Calcium binding site 4 out of 4 in the Structure of Calcineurin in Complex with NHE1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Calcineurin in Complex with NHE1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:27.4 occ:0.66 OD1 B:ASP100 2.0 28.4 1.0 O B:TYR106 2.0 30.1 1.0 OD1 B:ASP102 2.1 31.1 1.0 OE1 B:GLU111 2.1 25.7 1.0 OD1 B:ASP104 2.3 28.1 1.0 O B:HOH317 2.3 29.5 1.0 CD B:GLU111 3.0 27.1 1.0 CG B:ASP102 3.0 36.4 1.0 CG B:ASP104 3.1 35.3 1.0 CG B:ASP100 3.1 30.1 1.0 H B:TYR106 3.2 35.8 1.0 C B:TYR106 3.2 26.3 1.0 H B:ASP104 3.3 42.4 1.0 OE2 B:GLU111 3.3 25.1 1.0 OD2 B:ASP102 3.4 33.5 1.0 OD2 B:ASP104 3.5 32.6 1.0 H B:ASP102 3.6 36.5 1.0 HA B:ILE107 3.6 33.2 1.0 HA B:ASP100 3.6 35.4 1.0 H B:SER108 3.7 30.8 1.0 HG B:SER108 3.7 38.1 1.0 OD2 B:ASP100 3.8 29.0 1.0 N B:TYR106 3.9 29.8 1.0 HB2 B:TYR106 4.1 36.2 1.0 H B:LYS103 4.1 34.3 1.0 N B:ASP104 4.1 35.3 1.0 CA B:TYR106 4.1 27.4 1.0 N B:ILE107 4.2 26.2 1.0 CB B:ASP100 4.2 29.1 1.0 CA B:ASP100 4.2 29.4 1.0 CA B:ILE107 4.3 27.6 1.0 N B:SER108 4.3 25.6 1.0 CB B:ASP104 4.3 33.3 1.0 N B:ASP102 4.3 30.4 1.0 H B:GLY105 4.4 31.0 1.0 CB B:ASP102 4.4 30.4 1.0 N B:LYS103 4.4 28.6 1.0 HB2 B:ASP100 4.4 35.0 1.0 CG B:GLU111 4.4 25.3 1.0 HB2 B:SER108 4.5 35.2 1.0 OG B:SER108 4.5 31.7 1.0 C B:ASP100 4.5 29.8 1.0 HB3 B:ASP104 4.5 40.0 1.0 CB B:TYR106 4.6 30.2 1.0 CA B:ASP104 4.6 30.4 1.0 HG2 B:GLU111 4.7 30.4 1.0 CA B:ASP102 4.7 33.2 1.0 HG3 B:GLU111 4.7 30.4 1.0 C B:ILE107 4.7 25.9 1.0 C B:ASP102 4.7 29.3 1.0 N B:GLY105 4.7 25.8 1.0 H B:MET101 4.8 34.1 1.0 N B:MET101 4.8 28.4 1.0 O B:ASP100 4.9 28.3 1.0 C B:ASP104 4.9 30.1 1.0 HB3 B:ASP102 4.9 36.5 1.0 CB B:SER108 4.9 29.3 1.0 HB2 B:ASP102 4.9 36.5 1.0 H B:ILE107 5.0 31.4 1.0 HA B:TYR106 5.0 32.9 1.0 HB3 B:ASP100 5.0 35.0 1.0

R.Hendus-Altenburger, X.Wang, L.M.Sjogaard-Frich, E.Pedraz-Cuesta, S.R.Sheftic, A.H.Bendsoe, R.Page, B.B.Kragelund, S.F.Pedersen, W.Peti. Molecular Basis For the Binding and Selective Dephosphorylation of Na+/H+Exchanger 1 By Calcineurin. Nat Commun V. 10 3489 2019.
ISSN: ESSN 2041-1723
PubMed: 31375679
DOI: 10.1038/S41467-019-11391-7